Bryan, based on the gist output I think I have a candidate - please check that you’re not re-defining TMP or TMPDIR to a relative path - that would break pretty much anything. Check with
set | grep 'T*MP’ This must be either undefined or the paths *must* be absolute, i.e. start with a slash / Other replies below, but I think the above may be the main issue. On Mar 10, 2014, at 12:53 AM, Bryan Renne <[email protected]> wrote: > Hi Simon. Thank you for your reply. > > On Sun, Mar 9, 2014 at 6:41 PM, Simon Urbanek > <[email protected]> wrote: >> Bryan, >> >> On Mar 9, 2014, at 3:59 PM, Bryan Renne <[email protected]> wrote: >> >>> Thank you for your reply, Peter. >>> >>> On Sun, Mar 9, 2014 at 3:31 AM, peter dalgaard <[email protected]> wrote: >>>> >>>> On 09 Mar 2014, at 00:21 , Bryan Renne <[email protected]> wrote: >>>> >>>>> Hi there. I am having compilation problems with R 3.0.2 (and R 3.0.3) on >>>>> OS X 10.9.2. >>>> >>>> On homebrew.... (Would have been useful to say up front.) >>> >>> Actually, no. This is *not* a homebrew specific problem, >> >> It *is* as you even point yourself further down. It doesn't occur on a clean >> OS X system. > > OK, so to rule out any possible homebrew issues, I used the homebrew > uninstall script to delete homebrew and all homebrew-installed stuff > (https://gist.github.com/mxcl/1173223). This script wipes the system > clean of homebrew. > Thanks, it would be sufficient to just rename /usr/local and re-install the gfortran from CRAN. I cannot reproduce the issue with exactly your settings on a clean machine, so it must be some custom configuration of yours. I suspect you may have set TMP/TMPDIR to . which is invalid - please check. Thanks, Simon > I then installed gfortran 4.8.2 binaries using the provided pkg file > for OS X Mavericks (http://gcc.gnu.org/wiki/GFortranBinaries#MacOS). > > I then downloaded R-3.0.3.tar.gz from the main page > (http://cran.r-project.org/). I untarred, configured (with options > "--with-aqua --enable-R-framework --with-lapack") and ran make. I > received the same error as before. Here is the tail end of the "make" > output: > > begin installing recommended package MASS > Warning in read.dcf(fd <- file.path(pkg, "DESCRIPTION")) : > cannot open compressed file > './RtmpwOScIp/R.INSTALL588267e46267/MASS/DESCRIPTION', probable reason > 'No such file or directory' > Error: error reading file > './RtmpwOScIp/R.INSTALL588267e46267/MASS/DESCRIPTION' > make[2]: *** [MASS.ts] Error 1 > make[1]: *** [recommended-packages] Error 2 > make: *** [stamp-recommended] Error 2 > > Please see the following gist for full details of the system > configuration and output of "configure" and "make": > > https://gist.github.com/bprenne/9459571 > > In particular, you'll notice in the section for make the error I > quoted above. Also, at the very bottom of the gist, I have provided > what I think shows that the error is happening with the "R CMD INSTALL > MASS.tgz" step in the installation of recommended packages (somewhere > deep within the Makefile steps). > >>>>> [[...snip...] >>>>> I also tried setting R_INSTALL_TAR to the system tar or to a >>>>> homebrew-installed gnutar. Neither helped. >>>>> >>>>> Any suggestions on how I might proceed? >>>> >>>> Hmm, difficult to tell. If push comes to shove, you could try getting more >>>> info out of the INSTALL process (inject a >>>> debug(tools:::.install_packages), I suppose, but it is a bit beyond me >>>> currently). But first, I'd check what Makeconf sets the TAR variable to. >>> >>> Thank you for these suggestions. Makeconf contains this line: >>> >>> TAR = /usr/local/bin/gtar >>> >>> This is the homebrew-installed gnutar. However, is the R binary >>> (which has properly compiled and is the source of the error in library >>> installation) reading Makeconf to determine how to untar the library >>> .tgz? >>> >> >> No, it is set in etc/Renviron which is in turn populated via configure by >> the value you see in Makeconf. >> >> Try setting >> >> TAR=/usr/bin/tar >> >> since system tar normally works. But that may be only the tip of the >> iceberg, we can't tell what else you installed that breaks otherwise working >> system. If in doubt, share the list with us so we can try to replicate it. >> >> Cheers, >> Simon > > Thanks for this suggestion with setting the TAR variable. As you can > see from the gist (https://gist.github.com/bprenne/9459571), this is > now the default value because homebrew has been wiped from the system. > However, even with this value, the problem still obtains. > > I've tried to provide everything I can think will be useful in the gist. > > Is there something more I can provide or some way I can get more > fine-grained debugging information to help in diagnosis? > > I appreciate your time and any thoughts you might have that you think > would help. > _______________________________________________ R-SIG-Mac mailing list [email protected] https://stat.ethz.ch/mailman/listinfo/r-sig-mac
